The decision, in the aftermath of Nigeria's World Cup last 16 loss, came after a court sacked the NFF and the government appointed a sole administrator for the country's football shortly after the Super Eagles returned from Brazil.
"The FIFA Emergency Committee has decided today to suspend the Nigeria Football Federation (NFF) with immediate effect, on account of government interference," a FIFA statement explained.
Unless the suspension is lifted Nigeria will not be able to play in the upcoming FIFA Under-20 Women's World Cup scheduled for August 5-24 in Canada.
Nigerians expressed shock and disappointment over the suspension.
The country's Under-17 team, who are the defending world champions, are also in danger of missing out on the African Junior Championship next year in Niger as they have a qualifying match on July 20 in DR Congo.
Former Nigeria coach Christian Chukwu expressed disappointment over the ban saying "our football will suffer a lot as this can only take us backwards".
Former Lobi Stars and Akwa United coach Justin Tenger said it was a shame that Nigeria had to be told to do the right thing by FIFA.
"This is the saddest thing ever to happen to Nigerian football. It's too bad for another body to put our house in order for us, when we should organise ourselves better instead of what we are now witnessing."
A football stakeholder Aminu Kurfi demanded the resignation of Sports minister Tammy Danagogo for his alleged poor handling of the crisis that has rocked the country's football.
"We talked to top officials that we are doomed, but they refused to heed our sincere warning and this is where we now find ourselves," he said.
"The minister, a qualified lawyer, was misguided by those who ought to know better. He should quit on account of his poor handling of this matter."
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